9  Differences in microglia by sample & treatment

Published

August 28, 2025

9.1 Total microglia states

Uniform Manifold Approximation and Projection (UMAP) visualization of 29854 microglial cells.

Each point represents a single cell, and cells are colored according to unsupervised clusters identified from transcriptomic profiles.

9.2 Total cells

Bar plot showing the number of cells assigned to each cluster.

9.3 Gene Heatmap & hierarchical cluster

Heatmap of normalized expression levels for representative marker genes across clusters, with hierarchical clustering applied to both genes and clusters, providing an overview of the molecular signatures that distinguish microglial states.

9.4 Proportions (%) of Microglial States Across Samples and Treatments

Stacked barplot of the relative abundance of each microglial Seurat-defined cluster in individual samples and compared proportions between the Aducanumab-treated and IgG control groups.


Adu IgG p.overall
N=3 N=3
NFkB/IEG Activated 23.3 [22.0;23.8] 25.9 [24.8;26.1] 0.127
Homeostatic (Activation competent) 14.9 [14.9;15.1] 19.6 [18.5;20.1] 0.050
DAM (Early/Intermediate) 18.5 [17.4;19.0] 13.9 [13.3;14.4] 0.050
Remodeling / Injury response 12.5 [12.3;12.6] 11.1 [11.1;11.8] 0.268
Homeostatic (canonical) 10.6 [10.4;11.8] 11.1 [10.2;12.6] 0.827
DAM (late) 11.2 [9.80;12.3] 11.8 [11.5;11.9] 0.658
Antigen presenting 7.10 [4.30;7.10] 2.40 [2.40;4.20] 0.500
Interferon responsive 3.60 [3.25;3.70] 2.70 [2.65;2.90] 0.127
Proliferating 0.60 [0.45;0.80] 0.50 [0.45;0.55] 0.658

Values are median % of microglia in that cluster per sample, with IQR.
p.overall: Mann-Whitney p-value

9.5 Module scores

UMAP displaying the combined expression scores or the distribution of individual canonical microglial marker genes, illustrating the transcriptional features that define each cluster.

Markers from bibliography to generate the scores

Signature genes
AP Cp, H2-Eb1, H2-Ab1, H2-Aa, Cd74, B2m, Cd37
DAM Apoe, Trem2, Tyrobp, Lpl, Itgax, Cst7, Spp1, Clec7a, Ctsb, Ctsd, Fabp5, Lgals3
Homeostatic P2ry12, P2ry13, Cx3cr1, Maf, Frmd4a, Csf1r, Tmem119
IEG Fos, Jun, Junb, Egr1, Atf3, Ier2, Klf6, Arc, Dusp1, Nr4a1
IRM Ifit3, Ifit2, Isg15, Oasl2, Mx1, Stat1, Irf7, Rsad2, Gbp2, Gbp3, Ifi204
TIM Klf4, Malat1, Tmx4, Jund, Btg2, Jun, Fos, Klf2

IRM : Interferon-response microglia.
IEG : Intermediate early Gene-enriched
TIM : Terminally inflammatory microglia (Millet, Ledo, and Tavazoie 2024)
AP : Antigen Presenting